F8510 Physics of biopolyemers

Faculty of Science
Spring 2010
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Teacher(s)
prof. RNDr. Vladimír Vetterl, DrSc. (lecturer)
Guaranteed by
prof. RNDr. Vladimír Vetterl, DrSc.
Department of Condensed Matter Physics – Physics Section – Faculty of Science
Contact Person: prof. RNDr. Vladimír Vetterl, DrSc.
Timetable
Thu 15:00–16:50 BFU
Prerequisites (in Czech)
! Bi8510 Introduction to Molecular Biophysics
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
The main objective of the course is to provide the students with the ability to
- list and describe hydrodynamic, electric and magnetic properties of biopolymers
- apply this knowledge to explain the effects of electric, magnetic and electromagnetic fields on biopolymers and organisms.
Syllabus
  • 1. Introduction, structure and conformation of biopolymers 2.1. Chemical composition 2.2. Primary, secondary and tertiary structure 2.2.1. DNA as double-helix 2.2.2. Structure and conformation of proteins and polysacharides 2. Hydrodynamic properties 2.1. Viscosity 2.2. Sedimentation 2.3. Difussion 2.4. Osmotic pressure 3. Electric And Magnetic Properties of Nucleic Acids 3.1. Electric properties 3.1.1. Electronic charge distribution 3.1.2. Interactions of bases, nucleosides and nucleotides with ions 3.1.3. Forces stabilizing double helical conformation of DNA and synthetic polynucleotides 3.1.4. Electric field effects on DNA 3.2. Magnetic properties 4. Biomagnetism. Detection of magnetic fields produced by living organism. 4. Biological effects of electromagnetic fields. 4.1. Effects of extremely low frequency fields. 4.2. Effects of mobile phone frequencies.
Literature
  • HASOŇ, Stanislav, Hana PIVOŇKOVÁ, Vladimír VETTERL and Miroslav FOJTA. Label-free sequence-specific DNA sensing using copper-enhanced anodic stripping of purine bases at boron-doped diamond electrodes. Analytical Chemistry. USA: AMER CHEMICAL SOC, 1155 16TH ST, NW, WAS, 2008, 80/2008, No 7, p. 2391-2399. ISSN 0003-2700. info
  • HASOŇ, Stanislav, Vladimír VETTERL and Miroslav FOJTA. Two-dimensional condensation of pyrimidine oligonucleotides during their self-assemblies at mercury based surfaces. Electrochimica Acta. Amsterdam: Elsevier Science, 2008, vol. 53, No 1, p. 2818 - 2824. ISSN 0013-4686. info
  • AVRANAS, Antonis, Sofia KOURTIDU and Vladimír VETTERL. Adsorption of oligonucleotides A10, A25, A50 and A80 at the mercury/electrolyte interface. Colloids and Surfaces A: Physicochemical and Engineering Aspects. Amsterdam: Elsevier, 2007, vol. 295, March, p. 178-184. ISSN 0927-7765. info
  • VETTERL, Vladimír, Jiří VANĚK, Raimo SILVENNOINEN, Stanislav HASOŇ, Luděk STRAŠÁK, Pavlína ČERNOCHOVÁ, Patrik PRACHÁR, Sonia BARTÁKOVÁ, Ema JANČÁŘOVÁ and Stanislava MATALOVÁ. Biophysical approaches in dentistry. 2007. info
  • FOJT, Lukáš, Luděk STRAŠÁK and Vladimír VETTERL. Effect of electromagnetic fields on the denitrification activity of Paracoccus denitrificans. Bioelectrochemistry. The Netherlands: Elsevier, 2007, vol. 70, No 1, p. 91-95. ISSN 1567-5394. info
  • NOVÁK, Jan, Luděk STRAŠÁK, Lukáš FOJT, Iva SLANINOVÁ and Vladimír VETTERL. Effects of low-frequency magnetic fields on the viability of yeast Saccharomyces cerevisiae. Bioelectrochemistry. SWITZERLAND: Elsevier, 2007, vol. 70, x, p. 115-121. ISSN 1567-5394. info
  • KROUPOVÁ, Jana, Eva BÁRTOVÁ, Lukáš FOJT, Luděk STRAŠÁK, Stanislav KOZUBEK and Vladimír VETTERL. Low-frequency magnetic field effect on cytoskeleton and chromatin. Bioelectrochemistry. Elsevier, 2007, vol. 70, No 1, p. 96-100. ISSN 1567-5394. info
  • SILVENNOINEN, Raimo, Stanislav HASOŇ and Vladimír VETTERL. Organization of nano-scale synthetic oligonucleotides on immersed electrode surface: an optical study. In Technical digest. Tampere (Finland): University Joensuu, 2007, p. 101-102. info
  • VETTERL, Vladimír, Jiří VANĚK, Stanislav HASOŇ and Raimo SILVENNOINEN. Sensitive detection of oligonucleotides and their adsorption on amalgam and titanium surface. European Biophysics Journal. Berlin Heidelberg: Springer-Verlag, 2007, vol. 36, No 2007, p. 204. ISSN 1432-1017. info
  • VETTERL, Vladimír, Jiří VANĚK, Stanislav HASOŇ, Luděk STRAŠÁK and Lukáš FOJT. Adsorption of human blood plasma proteins on titanium implants. In 4th ISE Spring Meeting 2006, April 17-20, 2006, Singapore, Book of Abstracts. Singapore: International Society of Electrochemistry, 2006, p. 81. info
  • HASOŇ, Stanislav and Vladimír VETTERL. Amplified oligonucleotide sensing in microliter volumes containing copper ions by solution streaming. Analytical Chemistry. USA: AMER CHEMICAL SOC, 1155 16TH ST, NW, WAS, 2006, 78/2006, No 14, p. 5179-5183. ISSN 0003-2700. info
  • VETTERL, Vladimír. Biofyzika na prahu 2.tisíciletí. (Biophysics at the threshold of 2.millennium). Čs. čas. fyz. 2006, vol. 56, No 5, p. 284-287. ISSN 0009-0700. info
  • HASOŇ, Stanislav and Vladimír VETTERL. Detection of synthetic oligonucleotides by alternating current voltammetry at solid amalgam surfaces. Electrochimica Acta. UK: Pergamon, 2006, vol. 51, No 24, p. 5199-5205. ISSN 0013-4686. info
  • HASOŇ, Stanislav and Vladimír VETTERL. Microanalysis of oligodeoxynucleotides by cathodic stripping voltammetry at amalgam-alloy surfaces in the presence of copper ions. Talanta. Amsterdam: Elsevier Science, 2006, vol. 69, No 3, p. 572-580. ISSN 0039-9140. info
  • STRAŠÁK, Luděk, Lukáš FOJT, Iva SLANINOVÁ and Vladimír VETTERL. Effect of 50 Hz magnetic fields on yeasts Saccharomyces cerevisae. European Biophysics Journal. Berlin Heidelberg: Springer-Verlag, 2005, 34/2005, No 6, p. 773. ISSN 1432-1017. info
  • STRAŠÁK, Luděk, Vladimír VETTERL and Lukáš FOJT. Effects of 50 Hz magnetic fields on the viability of different bacterial strains. Electromagnetic Biology and Medicine. Philadelphia, USA: Taylor&Francis Inc., 2005, vol. 24, No 3, p. 293-300. ISSN 1536-8378. info
  • VETTERL, Vladimír and Jan IGNÁC. Self-assembled layers of nucleic acid bases and nucleosides at the interfaces and the origin of life. European Biophysics Journal. Berlin Heidelberg: Springer-Verlag, 2005, 34/2005, No 6, p. 639. ISSN 1432-1017. info
  • HASOŇ, Stanislav and Vladimír VETTERL. Application of thin film mercury electrodes and solid amalgam electrodes in electrochemical analysis of the nucleic acids components: detection of the two-dimensional phase transients of adenosine. Bioelectrochemistry. Elsevier, 2004, vol. 2004, No 63, p. 37-41. ISSN 1567-5394. info
  • FOJT, Lukáš, Luděk STRAŠÁK, Vladimír VETTERL and Jan ŠMARDA. Comparison of the low-frequency magnetic field effects on bacteria Escherichia coli, Leclercia adecarboxylata and Staphylococcus aureus. Bioelectrochemistry. 2004, vol. 2004, No 63, p. 337-341. ISSN 1567-5394. info
  • HASOŇ, Stanislav and Vladimír VETTERL. Detection of phase transients in two-dimensional adlayers of adenosine at the solid amalgam electrode surfaces. Journal of Electroanalytical Chemistry. Elsevier, 2004, vol. 2004, No 568, p. 65-77. ISSN 0022-0728. info
  • HASOŇ, Stanislav, Simo-Pekka SIMONAHO, Raimo SILVENNOINEN and Vladimír VETTERL. On the adsorption kinetics of phase transients of adenosine at the different carbon electrodes modified with a mercury layer. Electrochimica Acta. UK: Pergamon, 2003, vol. 48, No 1, p. 651-668. ISSN 0013-4686. info
  • HASOŇ, Stanislav and Vladimír VETTERL. Application of carbon electrodes modified with a mercury layer of a different thickness for studies of the adsorption and kinetics of phase transients of cytidine. Journal of Electroanalytical Chemistry. The Netherlands: Elsevier, 2002, vol. 536, No 1, p. 19-35. ISSN 0022-0728. info
  • STRAŠÁK, Luděk, Vladimír VETTERL and Jan ŠMARDA. Effects of low-frequency magnetic fields on bacteria Escherichia coli. Bioelectrochemistry. The Netherlands: Elsevier, 2002, vol. 2002, No 55, p. 161-164. ISSN 1567-5394. info
  • PALEČEK, Emil, Miroslav FOJTA, František JELEN and Vladimír VETTERL. Electrochemical analysis of nucleic acids. Weinheim: Wiley-VCH Verlag, 2002, 66 pp. Encyclopedia of Electrochemistry, Vol.9, p.365. ISBN 3-527-30401-0. info
  • HASOŇ, Stanislav, Jakub DVOŘÁK, František JELEN and Vladimír VETTERL. Impedance analysis of DNA and DNA-drug interactions on thin mercury film electrodes. Critical Reviews in Analytical Chemistry. Boca Raton (Florida, USA): CRC Press, 2002, vol. 32, No 2, p. 167-179. ISSN 1040-8347. info
  • HASOŇ, Stanislav, Jakub DVOŘÁK, František JELEN and Vladimír VETTERL. Interaction of DNA with echinomycin at the mercury electrode surface as detected by impedance and chronopotentiometric measurements. Talanta. Elsevier Science, 2002, vol. 56, No 5, p. 905-913. ISSN 0039-9140. info
  • HASOŇ, Stanislav and Vladimír VETTERL. On the formation kinetics of two-dimensional cytidine films. Bioelectrochemistry. The Netherlands: Elsevier, 2002, vol. 57, 1-2, p. 23-32. ISSN 1567-5394. info
  • HASOŇ, Stanislav and Vladimír VETTERL. Two-dimensional condensation of nucleic acid components at mercury film and gold electrodes. Bioelectrochemistry. The Netherlands: Elsevier, 2002, vol. 56, 1-2, p. 43-45. ISSN 1567-5394. info
  • JELEN, František, Vladimír VETTERL, Petr BĚLUŠA and Stanislav HASOŇ. Adsorptive Stripping Analysis of DNA with Admittance Detection. Electroanalysis. Weinheim: Wiley-VCH Verlag GmbH, 2000, vol. 12, No 12, p. 987-992. ISSN 1040-0397. info
  • VETTERL, Vladimír. Co je biofyzika ? (What is biophysics ?). Československý časopis pro fyziku. Praha: Fyzikální ústav AV ČR, 2000, vol. 50, No 6, p. 152-154. ISSN 0009-0700. info
  • DRAŽAN, Viktor and Vladimír VETTERL. Adsorption and condensation of xanthine at the mercury/solution interface. Collections of Czechoslovac Chemical Communications. Praha, 1998, vol. 63, No 1, p. 1977-1993. ISSN 0010-0765. info
  • FOJTA, Miroslav, Vladimír VETTERL, Miroslav TOMSCHIK, František JELEN and Peter NIELSEN. Adsorption of peptide nucleic acid and DNA decamers at electrically charged surfaces. Biophysical Journal. Amsterdam: Elsevier Scientific, 1997, vol. 1997, No 72, p. 2285-2293. info
  • BRABEC, Viktor, Vladimír KLEINWÄCHTER and Vladimír VETTERL. Structure, chemical reactivity and electromagnetic properties of nucleic acids. In Bioelectrochemistry: Principles and Practice. Basel, Switzerland: Birkhäuser Verlag, 1997, p. 1-104. 5. ISBN 3-7643-5296-5. info
  • BRABEC, Vladimír, V. KLEINWACHTER and Vladimír VETTERL. Struktura, chemická reaktivita a elektromagnetické vlastnosti nukleových kyselin (Structure, chemical reactivity and electromagnetic properties of nucleic acids). In Biochemistry and biomacromolecules. Basel: Birghauser Verlag, 1997, p. 1-104. 5. ISBN 3-7643-5084-9. info
  • ŠPONER, Jiří, J. LESZCZYNSKI, Vladimír VETTERL and P. HOBZA. Base stacking and hydrgen bonding in protonated cytosine dimer: the role of molecular ion-dipole and induction interaction. J.Biomol. Struct. Dyn. 1996, vol. 1996, No 13, p. 695-706. ISSN 0739-1102. info
  • JURÁŠKOVÁ, V., Vladimír VETTERL and O. CHRAMOSTA. Effect of cadmium and 50 Hz electric and magnetic fields on bobe marrow and tumour cells. Bioelectrochem.Bioenerg. 1996, vol. 1996, No 39, p. 119-123. ISSN 0302-4598. info
  • VETTERL, Vladimír. Platí zákony fyziky i u živých organismů? (Are the physical laws valid for living organisms?). Čs. čas. fyz. 1996, vol. 1996, No 46, p. 170-173. ISSN 0009-0700. info
Teaching methods
lectures, class discussion
Assessment methods
1 written test, oral exam.
Language of instruction
Czech
Further Comments
Study Materials
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.
  • Enrolment Statistics (Spring 2010, recent)
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